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Khurshaid N, Shabir N, Pala AH, Yadav AK, Singh D, Ashraf N. Transcriptome wide analysis of MADS box genes in Crocus sativus and interplay of CstMADS19-CstMADS26 in orchestrating apocarotenoid biosynthesis. Gene 2024; 932:148893. [PMID: 39197797 DOI: 10.1016/j.gene.2024.148893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/09/2024] [Accepted: 08/23/2024] [Indexed: 09/01/2024]
Abstract
Flowers of Crocus sativus L. are immensely important not only for arrangement of floral whorls but more because each floral organ is dominated by a different class of specialized compounds. Dried stigmas of C. sativus flowers form commercial saffron, and are known to accumulate unique apocarotenoids like crocin, picrocrocin and safranal. Inspite of being a high value crop, the molecular mechanism regulating flower development in Crocus remains largely unknown. Moreover, it would be very interesting to explore any co-regulatory mechanism which controls floral architecture and secondary metabolic pathways which exist in specific floral organs. Here we report transcriptome wide identification of MADS box genes in Crocus. A total of 39 full length MADS box genes were identified among which three belonged to type I and 36 to type II class. Phylogeny classified them into 11 sub-clusters. Expression pattern revealed some stigma up-regulated genes among which CstMADS19 encoding an AGAMOUS gene showed high expression. Transient over-expression of CstMADS19 in stigmas of Crocus resulted in increased crocin by enhancing expression of pathway genes. Yeast one hybrid assay demonstrated that CstMADS19 binds to promoters of phytoene synthase and carotenoid cleavage dioxygenase 2 genes. Yeast two hybrid and BiFC assays confirmed interaction of CstMADS19 with CstMADS26 which codes for a SEPALATA gene. Co-overexpression of CstMADS19 and CstMADS26 in Crocus stigmas enhanced crocin content more than was observed when genes were expressed individually. Collectively, these findings indicate that CstMADS19 functions as a positive regulator of stigma based apocarotenoid biosynthesis in Crocus.
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Affiliation(s)
- Nargis Khurshaid
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine (IIIM), Sanat Nagar, Srinagar, Jammu and Kashmir 190005, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India
| | - Najwa Shabir
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine (IIIM), Sanat Nagar, Srinagar, Jammu and Kashmir 190005, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India
| | - Aamir Hussain Pala
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine (IIIM), Sanat Nagar, Srinagar, Jammu and Kashmir 190005, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India
| | - Arvind Kumar Yadav
- Quality Control & Quality Assurance Lab, Quality, Management & Instrumentation Division, CSIR- Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Deepika Singh
- Quality Control & Quality Assurance Lab, Quality, Management & Instrumentation Division, CSIR- Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Nasheeman Ashraf
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine (IIIM), Sanat Nagar, Srinagar, Jammu and Kashmir 190005, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India.
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2
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Sun Y, Dong L, Kang L, Zhong W, Jackson D, Yang F. Progressive meristem and single-cell transcriptomes reveal the regulatory mechanisms underlying maize inflorescence development and sex differentiation. MOLECULAR PLANT 2024; 17:1019-1037. [PMID: 38877701 DOI: 10.1016/j.molp.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely unclear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel, we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. We identified 16 diverse gene clusters with differential spatiotemporal expression patterns and revealed biased regulation of redox, programmed cell death, and hormone signals during meristem differentiation between ear and tassel. Notably, based on their dynamic expression patterns, we revealed the roles of two RNA-binding proteins in regulating inflorescence meristem activity and axillary meristem formation. Moreover, using the transcriptional profiles of 53 910 single cells, we uncovered the cellular heterogeneity between ear and tassel florets. We found that multiple signals associated with either enhanced cell death or reduced growth are responsible for tassel pistil suppression, while part of the gibberellic acid signal may act non-cell-autonomously to regulate ear stamen arrest during sex differentiation. We further showed that the pistil-protection gene SILKLESS 1 (SK1) functions antagonistically to the known pistil-suppression genes through regulating common molecular pathways, and constructed a regulatory network for pistil-fate determination. Collectively, our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation for identifying new regulators and pathways for maize hybrid breeding and improvement.
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Affiliation(s)
- Yonghao Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Liang Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; School of Agriculture, Sun Yat-Sen University, Shenzhen 518107, China.
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Jiu S, Manzoor MA, Chen B, Xu Y, Abdullah M, Zhang X, Lv Z, Zhu J, Cao J, Liu X, Wang J, Liu R, Wang S, Dong Y, Zhang C. Chromosome-level genome assembly provides insights into the genetic diversity, evolution, and flower development of Prunus conradinae. MOLECULAR HORTICULTURE 2024; 4:25. [PMID: 38898491 PMCID: PMC11186256 DOI: 10.1186/s43897-024-00101-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Prunus conradinae, a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic to China, has high economic and ornamental value. However, a high-quality P. conradinae genome is unavailable, which hinders our understanding of its genetic relationships and phylogenesis, and ultimately, the possibility of mining of key genes for important traits. Herein, we have successfully assembled a chromosome-scale P. conradinae genome, identifying 31,134 protein-coding genes, with 98.22% of them functionally annotated. Furthermore, we determined that repetitive sequences constitute 46.23% of the genome. Structural variation detection revealed some syntenic regions, inversions, translocations, and duplications, highlighting the genetic diversity and complexity of Cerasus. Phylogenetic analysis demonstrated that P. conradinae is most closely related to P. campanulata, from which it diverged ~ 19.1 million years ago (Mya). P. avium diverged earlier than P. cerasus and P. conradinae. Similar to the other Prunus species, P. conradinae underwent a common whole-genome duplication event at ~ 138.60 Mya. Furthermore, 79 MADS-box members were identified in P. conradinae, accompanied by the expansion of the SHORT VEGETATIVE PHASE subfamily. Our findings shed light on the complex genetic relationships, and genome evolution of P. conradinae and will facilitate research on the molecular breeding and functions of key genes related to important horticultural and economic characteristics of subgenus Cerasus.
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Affiliation(s)
- Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Baozheng Chen
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming, China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jijun Zhu
- Shanghai Botanical Garden, Shanghai, People's Republic of China
| | - Jun Cao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Dong
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming, China.
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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Liu Y, Guan C, Chen Y, Shi Y, Long O, Lin H, Zhang K, Zhou M. Evolutionary analysis of MADS-box genes in buckwheat species and functional study of FdMADS28 in flavonoid metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108637. [PMID: 38670031 DOI: 10.1016/j.plaphy.2024.108637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
The MADS-box gene family is a transcription factor family that is widely expressed in plants. It controls secondary metabolic processes in plants and encourages the development of tissues like roots and flowers. However, the phylogenetic analysis and evolutionary model of MADS-box genes in Fagopyrum species has not been reported yet. This study identified the MADS-box genes of three buckwheat species at the whole genome level, and conducted systematic evolution and physicochemical analysis. The results showed that these genes can be divided into four subfamilies, with fragment duplication being the main way for the gene family expansion. During the domestication process from golden buckwheat to tartary buckwheat and the common buckwheat, the Ka/Ks ratio indicated that most members of the family experienced strong purification selection pressure, and with individual gene pairs experiencing positive selection. In addition, we combined the expression profile data of the MADS genes, mGWAS data, and WGCNA data to mine genes FdMADS28/48/50 that may be related to flavonoid metabolism. The results also showed that overexpression of FdMADS28 could increase rutin content by decreasing Kaempferol pathway content in hairy roots, and increase the resistance and growth of hairy roots to PEG and NaCl. This study systematically analyzed the evolutionary relationship of MADS-box genes in the buckwheat species, and elaborated on the expression patterns of MADS genes in different tissues under biotic and abiotic stresses, laying an important theoretical foundation for further elucidating their role in flavonoid metabolism.
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Affiliation(s)
- Yang Liu
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaonan Guan
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanyuan Chen
- College of Agriculture, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Yaliang Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ou Long
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meiliang Zhou
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Song GQ, Liu Z, Zhong GY. Regulatory frameworks involved in the floral induction, formation and developmental programming of woody horticultural plants: a case study on blueberries. FRONTIERS IN PLANT SCIENCE 2024; 15:1336892. [PMID: 38410737 PMCID: PMC10894941 DOI: 10.3389/fpls.2024.1336892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Flowering represents a crucial stage in the life cycles of plants. Ensuring strong and consistent flowering is vital for maintaining crop production amidst the challenges presented by climate change. In this review, we summarized key recent efforts aimed at unraveling the complexities of plant flowering through genetic, genomic, physiological, and biochemical studies in woody species, with a special focus on the genetic control of floral initiation and activation in woody horticultural species. Key topics covered in the review include major flowering pathway genes in deciduous woody plants, regulation of the phase transition from juvenile to adult stage, the roles of CONSTANS (CO) and CO-like gene and FLOWERING LOCUS T genes in flower induction, the floral regulatory role of GA-DELLA pathway, and the multifunctional roles of MADS-box genes in flowering and dormancy release triggered by chilling. Based on our own research work in blueberries, we highlighted the central roles played by two key flowering pathway genes, FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, which regulate floral initiation and activation (dormancy release), respectively. Collectively, our survey shows both the conserved and diverse aspects of the flowering pathway in annual and woody plants, providing insights into the potential molecular mechanisms governing woody plants. This paves the way for enhancing the resilience and productivity of fruit-bearing crops in the face of changing climatic conditions, all through the perspective of genetic interventions.
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Affiliation(s)
- Guo-Qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Zongrang Liu
- USDA Agricultural Research Services, Appalachian Fruit Research Station, Kearneysville, WV, United States
| | - Gan-Yuan Zhong
- USDA Agricultural Research Services, Grape Genetics Research Unit and Plant Genetic Resources Unit, Geneva, NY, United States
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Lin Y, Qi X, Wan Y, Chen Z, Fang H, Liang C. Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model. BMC Genomics 2023; 24:447. [PMID: 37553575 PMCID: PMC10408238 DOI: 10.1186/s12864-023-09509-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/08/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Lonicera japonica Thunb. is widely used in traditional Chinese medicine. Medicinal L. japonica mainly consists of dried flower buds and partially opened flowers, thus flowers are an important quality indicator. MADS-box genes encode transcription factors that regulate flower development. However, little is known about these genes in L. japonica. RESULTS In this study, 48 MADS-box genes were identified in L. japonica, including 20 Type-I genes (8 Mα, 2 Mβ, and 10 Mγ) and 28 Type-II genes (26 MIKCc and 2 MIKC*). The Type-I and Type-II genes differed significantly in gene structure, conserved domains, protein structure, chromosomal distribution, phylogenesis, and expression pattern. Type-I genes had a simpler gene structure, lacked the K domain, had low protein structure conservation, were tandemly distributed on the chromosomes, had more frequent lineage-specific duplications, and were expressed at low levels. In contrast, Type-II genes had a more complex gene structure; contained conserved M, I, K, and C domains; had highly conserved protein structure; and were expressed at high levels throughout the flowering period. Eleven floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in L. japonica. By integrating expression pattern and protein interaction data for these genes, we developed a possible model for floral organ identity determination. CONCLUSION This study genome-widely identified and characterized the MADS-box gene family in L. japonica. Eleven floral homeotic MADS-box genes were identified and a possible model for floral organ identity determination was also developed. This study contributes to our understanding of the MADS-box gene family and its possible involvement in floral organ development in L. japonica.
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Affiliation(s)
- Yi Lin
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yan Wan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zequn Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Hailing Fang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Chengyuan Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China.
- Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Jiu S, Chen B, Dong X, Lv Z, Wang Y, Yin C, Xu Y, Zhang S, Zhu J, Wang J, Liu X, Sun W, Yang G, Li M, Li S, Zhang Z, Liu R, Wang L, Manzoor MA, José QG, Wang S, Lei Y, Yang L, Dirlewanger E, Dong Y, Zhang C. Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L. HORTICULTURE RESEARCH 2023; 10:uhad062. [PMID: 37220556 PMCID: PMC10200261 DOI: 10.1093/hr/uhad062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/02/2023] [Indexed: 05/25/2023]
Abstract
Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.
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Affiliation(s)
| | | | - Xiao Dong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yuxuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunjin Yin
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Sen Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Jijun Zhu
- Shanghai Botanical Garden, Shanghai, 200231, P. R. China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Guoqian Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Meng Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu Province, 200037, P. R. China
| | - Shufeng Li
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Zhuo Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Quero-García José
- INRAe, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d'Ornon, France
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yahui Lei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Ling Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
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Suetsugu K, Fukushima K, Makino T, Ikematsu S, Sakamoto T, Kimura S. Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia. THE NEW PHYTOLOGIST 2023; 237:323-338. [PMID: 36110047 DOI: 10.1111/nph.18495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Cleistogamy, in which plants can reproduce via self-fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy - the production of only cleistogamous flowers - has rarely been recognized. Thus far, the achlorophyllous orchid genus, Gastrodia, is the only known genus with several plausible completely cleistogamous species. Here, we analyzed the floral developmental transcriptomes of two recently evolved, completely cleistogamous Gastrodia species and their chasmogamous sister species to elucidate the possible changes involved in producing common cleistogamous traits. The ABBA-BABA test did not support introgression and protein sequence convergence as evolutionary mechanisms leading to cleistogamy, leaving convergence in gene expression as a plausible mechanism. Regarding transcriptomic differentiation, the two cleistogamous species had common modifications in the expression of developmental regulators, exhibiting a gene family-wide signature of convergent expression changes in MADS-box genes. Our transcriptomic pseudotime analysis revealed a prolonged juvenile state and eventual maturation, a heterochronic pattern consistent with partial neoteny, in cleistogamous flower development. These findings indicate that transcriptomic partial neoteny, arising from changes in the expression of conserved developmental regulators, might have contributed to the rapid and repeated evolution of cleistogamous flowers in Gastrodia.
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Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, 97082, Würzburg, Germany
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, 6-3, Aramaki Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Shuka Ikematsu
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Tomoaki Sakamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
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9
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Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii. Nat Commun 2022; 13:7328. [PMID: 36443323 PMCID: PMC9705720 DOI: 10.1038/s41467-022-35063-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
Tree peony (Paeonia ostii) is an economically important ornamental plant native to China. It is also notable for its seed oil, which is abundant in unsaturated fatty acids such as α-linolenic acid (ALA). Here, we report chromosome-level genome assembly (12.28 Gb) of P. ostii. In contrast to monocots with giant genomes, tree peony does not appear to have undergone lineage-specific whole-genome duplication. Instead, explosive LTR expansion in the intergenic regions within a short period (~ two million years) may have contributed to the formation of its giga-genome. In addition, expansion of five types of histone encoding genes may have helped maintain the giga-chromosomes. Further, we conduct genome-wide association studies (GWAS) on 448 accessions and show expansion and high expression of several genes in the key nodes of fatty acid biosynthetic pathway, including SAD, FAD2 and FAD3, may function in high level of ALAs synthesis in tree peony seeds. Moreover, by comparing with cultivated tree peony (P. suffruticosa), we show that ectopic expression of class A gene AP1 and reduced expression of class C gene AG may contribute to the formation of petaloid stamens. Genomic resources reported in this study will be valuable for studying chromosome/genome evolution and tree peony breeding.
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10
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Choi BS, Choi SK, Kim NS, Choi IY. NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer. Genomics Inform 2022; 20:e40. [PMID: 36239113 PMCID: PMC9576473 DOI: 10.5808/gi.21075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 12/31/2022] Open
Abstract
BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.
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Affiliation(s)
| | - Seon Kang Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Soo Kim
- BIT Institute NBIT Co., Ltd., Chuncheon 24341, Korea
| | - Ik-Young Choi
- BIT Institute NBIT Co., Ltd., Chuncheon 24341, Korea
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
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11
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Wu Z, Huang L, Huang F, Lu G, Wei S, Liu C, Deng H, Liang G. Temporal transcriptome analysis provides molecular insights into flower development in red-flesh pitaya. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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12
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Lin Z, Cao D, Damaris RN, Yang P. Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus ( Nelumbo nucifera). PeerJ 2021; 9:e12322. [PMID: 34754621 PMCID: PMC8552788 DOI: 10.7717/peerj.12322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/25/2021] [Indexed: 11/20/2022] Open
Abstract
Lotus (Nelumbo nucifera) is a highly recognized flower with high ornamental value. Flower color and flower morphology are two main factors for flower lotus breeding. Petaloidy is a universal phenomenon in lotus flowers. However, the genetic regulation of floral organ petaloidy in lotus remains elusive. In this study, the transcriptomic analysis was performed among three organs, including petal, carpel petaloidy, and carpel in lotus. A total of 1,568 DEGs related to carpel petaloidy were identified. Our study identified one floral homeotic gene encoded by the MADS-box transcription factor, AGAMOUS (AG) as the candidate gene for petaloid in lotus. Meanwhile, a predicted labile boundary in floral organs of N. nucifera was hypothesized. In summary, our results explored the candidate genes related to carpel petaloidy, setting a theoretical basis for the molecular regulation of petaloid phenotype.
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Affiliation(s)
- Zhongyuan Lin
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Dingding Cao
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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13
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Song GQ, Han X, Ryner JT, Thompson A, Wang K. Utilizing MIKC-type MADS-box protein SOC1 for yield potential enhancement in maize. PLANT CELL REPORTS 2021; 40:1679-1693. [PMID: 34091722 PMCID: PMC8376726 DOI: 10.1007/s00299-021-02722-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/25/2021] [Indexed: 05/26/2023]
Abstract
Overexpression of Zea mays SOC gene promotes flowering, reduces plant height, and leads to no reduction in grain production per plant, suggesting enhanced yield potential, at least, through increasing planting density. MIKC-type MADS-box gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) is an integrator conserved in the plant flowering pathway. In this study, the maize SOC1 (ZmSOC1) gene was cloned and overexpressed in transgenic maize Hi-II genotype. The T0 plants were backcrossed with nontransgenic inbred B73 to produce first generation backcross (BC1) seeds. Phenotyping of both transgenic and null segregant (NT) BC1 plants was conducted in three independent experiments. The BC1 transgenic plants showed new attributes such as increased vegetative growth, accelerated flowering time, reduced overall plant height, and increased grain weight. Second generation backcross (BC2) plants were evaluated in the field using two planting densities. Compared to BC2 NT plants, BC2 transgenic plants, were 12-18% shorter, flowered 5 days earlier, and showed no reduction in grain production per plant and an increase in fat, starch, and simple sugars in the grain. Transcriptome comparison in young leaves of 56-day-old BC1 plants revealed that the overexpressed ZmSOC1 resulted in 107 differentially expressed genes. The upregulated transcription factor DNA BINDING WITH ONE FINGER 5.4 (DOF5.4) was among the genes responsible for the reduced plant height. Modulating expression of SOC1 opens a new and effective approach to promote flowering and reduce plant height, which may have potential to enhance crop yield and improve grain quality.
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Affiliation(s)
- Guo-Qing Song
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI, 48824, USA.
| | - Xue Han
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI, 48824, USA
| | - John T Ryner
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Addie Thompson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Kan Wang
- Department of Agronomy, Crop Bioengineering Center, Iowa State University, Ames, IA, 50011-1051, USA
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14
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De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families. Sci Rep 2021; 11:16246. [PMID: 34376711 PMCID: PMC8355218 DOI: 10.1038/s41598-021-95085-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
The Royal Irises (section Oncocyclus) are a Middle-Eastern group of irises, characterized by extremely large flowers with a huge range of flower colors and a unique pollination system. The Royal Irises are considered to be in the course of speciation and serve as a model for evolutionary processes of speciation and pollination ecology. However, no transcriptomic and genomic data are available for these plants. Transcriptome sequencing is a valuable resource for determining the genetic basis of ecological-meaningful traits, especially in non-model organisms. Here we describe the de novo transcriptome assembly of Iris atropurpurea, an endangered species endemic to Israel's coastal plain. We sequenced and analyzed the transcriptomes of roots, leaves, and three stages of developing flower buds. To identify genes involved in developmental processes we generated phylogenetic gene trees for two major gene families, the MADS-box and MYB transcription factors, which play an important role in plant development. In addition, we identified 1503 short sequence repeats that can be developed for molecular markers for population genetics in irises. This first reported transcriptome for the Royal Irises, and the data generated, provide a valuable resource for this non-model plant that will facilitate gene discovery, functional genomic studies, and development of molecular markers in irises, to complete the intensive eco-evolutionary studies of this group.
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15
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Song GQ, Han X. K-Domain Technology: Constitutive Expression of a Blueberry Keratin-Like Domain Mimics Expression of Multiple MADS-Box Genes in Enhancing Maize Grain Yield. FRONTIERS IN PLANT SCIENCE 2021; 12:664983. [PMID: 34025703 PMCID: PMC8137907 DOI: 10.3389/fpls.2021.664983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/15/2021] [Indexed: 06/02/2023]
Abstract
MADS-box genes are considered as the foundation of all agronomic traits because they play essential roles in almost every aspect of plant reproductive development. Keratin-like (K) domain is a conserved protein domain of tens of MIKC-type MADS-box genes in plants. K-domain technology constitutively expresses a K-domain to mimic expression of the K-domains of other MADS-box genes simultaneously and thus to generate new opportunities for yield enhancement, because the increased K-domains can likely prevent MADS-domain proteins from binding to target DNA. In this study, we evaluated utilizing the K-domain technology to increase maize yield. The K-domain of a blueberry's SUPPRESSOR of CONSTITUTIVE EXPRESSION OF CONSTANS 1 (VcSOC1K) has similarities to five MADS-box genes in maize. Transgenic maize plants expressing the VcSOC1K showed 13-100% of more grain per plant than the nontransgenic plants in all five experiments conducted under different experimental conditions. Transcriptome comparisons revealed 982 differentially expressed genes (DEGs) in the leaves from 83-day old plants, supporting that the K-domain technology were powerful and multiple functional. The results demonstrated that constitutive expression of the VcSOC1K was very effective to enhance maize grain production. With the potential of mimicking the K-domains of multiple MADS-box genes, the K-domain technology opens a new approach to increase crop yield.
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16
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An Optimized Transformation System and Functional Test of CYC-Like TCP Gene CpCYC in Chirita pumila (Gesneriaceae). Int J Mol Sci 2021; 22:ijms22094544. [PMID: 33925272 PMCID: PMC8123712 DOI: 10.3390/ijms22094544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/17/2022] Open
Abstract
The development of an ideal model plant located at a key phylogenetic node is critically important to advance functional and regulatory studies of key regulatory genes in the evolutionary developmental (evo-devo) biology field. In this study, we selected Chirita pumila in the family Gesneriaceae, a basal group in Lamiales, as a model plant to optimize its genetic transformation system established previously by us through investigating a series of factors and further conduct functional test of the CYC-like floral symmetry gene CpCYC. By transforming a RNAi:CpCYC vector, we successfully achieved the desired phenotypes of upright actinomorphic flowers, which suggest that CpCYC actually determines the establishment of floral zygomorphy and the horizontal orientation of flowers in C. pumila. We also confirmed the activities of CpCYC promoter in dorsal petals, dorsal/lateral staminodes, as well as the pedicel by transferring a CpCYC promoter:GUS vector into C. pumila. Furthermore, we testified the availability of a transient gene expression system using C. pumila mesophyll protoplasts. The improved transformation system together with the inherent biological features would make C. pumila an attractive new model in functional and regulatory studies for a broad range of evo-devo issues.
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17
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Genetic and comparative mapping of Lupinus luteus L. highlight syntenic regions with major orthologous genes controlling anthracnose resistance and flowering time. Sci Rep 2020; 10:19174. [PMID: 33154532 PMCID: PMC7645761 DOI: 10.1038/s41598-020-76197-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/23/2020] [Indexed: 01/12/2023] Open
Abstract
Anthracnose susceptibility and ill-adapted flowering time severely affect Lupinus luteus yield, which has high seed protein content, is excellent for sustainable agriculture, but requires genetic improvement to fulfil its potential. This study aimed to (1) develop a genetic map; (2) define collinearity and regions of synteny with Lupinus angustifolius; and (3) map QTLs/candidate genes for anthracnose resistant and flowering time. A few linkage groups/genomic regions tended to be associated with segregation distortion, but did not affect the map. The developed map showed collinearity, and syntenic regions with L. angustifolius. Major QTLs were mapped in syntenic regions. Alleles from the wild parent and cultivar, explained 75% of the phenotypic variance for anthracnose resistance and 83% for early flowering, respectively. Marker sequences flanking the QTLs showed high homology with the Lanr1 gene and Flowering-locus-T of L. angustifolius. This suggests orthologous genes for both traits in the L. luteus genome. The findings are remarkable, revealing the potential to combine early flowering/anthracnose resistant in fulfilling yield capacity in L. luteus, and can be a major strategy in the genetic improvement and usage of this species for sustainable protein production. Allele sequences and PCR-marker tagging of these genes are being applied in marker assisted selection.
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18
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Hui WK, Liu MQ, Wu GJ, Wang JY, Zhong Y, Li HY, Tang HL, Zeng W, Ma LX, Zhang Y, Xiang L, Chen XY, Gong W. Ectopic expression of an AGAMOUS homologue gene in Jatropha curcas causes early flowering and heterostylous phenotypes. Gene 2020; 766:145141. [PMID: 32911031 DOI: 10.1016/j.gene.2020.145141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 01/06/2023]
Abstract
Jatropha curcasseeds are abundant in biodiesel, and low seed yields are linked to poor quality female flowers, which creates a bottleneck for Jatropha seed utilization. Therefore, identifying the genes associated with flowering is crucial for the genetic enrichment of seed yields. Here, we identified an AGAMOUS homologue gene (JcAG) from J. curcas. We found that reproductive organs had higher JcAG expression than vegetative organs, particularly the carpel. Rosette leaves were small and misshapen in 35S:JcAG transgenic lines in comparison with those in wild-type plants. JcAG overexpression caused an extremely early flowering, delayed perianth and stamen filament development, small flowers, and significantly shorter Arabidopsis plants with little fruit. In the JcAG-overexpressing line, the homeotic transformation of sepals into pistillate organs was observed, and floral meristem and organ identity genes were regulated. This study provides insights into the JcAG's function and benefits to our knowledge of the underlying the genetic mechanisms related to floral sex differentiation in Jatropha.
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Affiliation(s)
- Wen-Kai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Ming-Qian Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, Preparation Office of South China Agricultural Museum, South China Agricultural University, Guangzhou 510642, China
| | - Guo-Jiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jing-Yan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - He-Yue Li
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Hai-Long Tang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Zeng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Le-Xun Ma
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Xiang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiao-Yang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, Preparation Office of South China Agricultural Museum, South China Agricultural University, Guangzhou 510642, China.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China.
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19
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Rodríguez-Cazorla E, Ripoll JJ, Ortuño-Miquel S, Martínez-Laborda A, Vera A. Dissection of the Arabidopsis HUA-PEP gene activity reveals that ovule fate specification requires restriction of the floral A-function. THE NEW PHYTOLOGIST 2020; 227:1222-1234. [PMID: 32259283 DOI: 10.1111/nph.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Ovules are essential for sexual plant reproduction and seed formation, and are fundamental for agriculture. However, our understanding of the molecular mechanisms governing ovule development is far from complete. In Arabidopsis, ovule identity is determined by homeotic MADS-domain proteins that define the floral C- (AG) and D- (SHP1/SHP2, STK) functions. Pre-mRNA processing of these genes is critical and mediated by HUA-PEP activity, composed of genes encoding RNA-binding proteins. In strong hua-pep mutants, functional transcripts for C- and D-function genes are reduced, resulting in homeotic transformation of ovules. Thus, hua-pep mutants provide an unique sensitized background to study ovule morphogenesis when C- and D-functions are simultaneously compromised. We found that hua-pep ovules are morphologically sepaloid and show ectopic expression of the homeotic class-A gene AP1. Inactivation of AP1 or AP2 (A-function genes) in hua-pep mutants reduced homeotic conversions, rescuing ovule identity while promoting carpelloid traits in transformed ovules. Interestingly, increased AG dosage led to similar results. Our findings strongly suggest that HUA-PEP activity is required for correct C and D floral functions, which in turn prevents ectopic expression of class-A genes in ovules for their proper morphogenesis, evoking the classic A-C antagonism of the ABC model for floral organ development.
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Affiliation(s)
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- TATA Institute for Genetics and Society (TIGS), University of California San Diego, La Jolla, CA, 92093, USA
| | - Samanta Ortuño-Miquel
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain
| | | | - Antonio Vera
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain
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20
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Villar L, Lienqueo I, Llanes A, Rojas P, Perez J, Correa F, Sagredo B, Masciarelli O, Luna V, Almada R. Comparative transcriptomic analysis reveals novel roles of transcription factors and hormones during the flowering induction and floral bud differentiation in sweet cherry trees (Prunus avium L. cv. Bing). PLoS One 2020; 15:e0230110. [PMID: 32163460 PMCID: PMC7067470 DOI: 10.1371/journal.pone.0230110] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 02/22/2020] [Indexed: 12/13/2022] Open
Abstract
In sweet cherry trees, flowering is commercially important because the flowers, after fertilization, will generate the fruits. In P. avium, the flowering induction and flower organogensis are the first developmental steps towards flower formation and they occur within specialized organs known as floral buds during the summer, nine months before blooming. During this period the number of floral buds per tree and the bud fruitfulness (number of flowers per bud) are stablished affecting the potential yield of orchards and the plant architecture. The floral bud development is sensitive to any type of stress and the hotter and drier summers will interfere with this process and are calling for new adapted cultivars. A better understanding of the underlying molecular and hormonal mechanisms would be of help, but unlike the model plant Arabidopsis, very little is known about floral induction in sweet cherry. To explore the molecular mechanism of floral bud differentiation, high-throughput RNA sequencing was used to detect differences in the gene expression of P. avium floral buds at five differentiation stages. We found 2,982 differentially expressed genes during floral bud development. We identified genes associated with floral initiation or floral organ identity that appear to be useful biomarkers of floral development and several transcription factor families (ERF, MYB, bHLH, MADS-box and NAC gene family) with novel potential roles during floral transition in this species. We analyzed in deep the MADS-box gene family and we shed light about their key role during floral bud and organs development in P. avium. Furthermore, the hormonal-related signatures in the gene regulatory networks and the dynamic changes of absicic acid, zeatin and indolacetic acid contents in buds suggest an important role for these hormones during floral bud differentiation in sweet cherry. These data provide a rich source of novel informacion for functional and evolutionary studies about floral bud development in sweet cherry and new tools for biotechnology and breeding.
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Affiliation(s)
- Luis Villar
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Ixia Lienqueo
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Analía Llanes
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Pamela Rojas
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Jorge Perez
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Francisco Correa
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Rengo, Chile
| | - Oscar Masciarelli
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Virginia Luna
- Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Rubén Almada
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
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21
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Zhang X, Pan BZ, Chen M, Chen W, Li J, Xu ZF, Liu C. JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants. BMC Genomics 2019; 20:958. [PMID: 31874631 PMCID: PMC6929279 DOI: 10.1186/s12864-019-6356-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 11/29/2019] [Indexed: 12/02/2022] Open
Abstract
Background Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energy plants. With the development of high-throughput sequencing, the genome of Jatropha curcas has been sequenced by different groups and a mass of transcriptome data was released. How to integrate and analyze these omics data is crucial for functional genomics research on J. curcas. Results By establishing pipelines for processing novel gene identification, gene function annotation, and gene network construction, we systematically integrated and analyzed a series of J. curcas transcriptome data. Based on these data, we constructed a J. curcas database (JCDB), which not only includes general gene information, gene functional annotation, gene interaction networks, and gene expression matrices but also provides tools for browsing, searching, and downloading data, as well as online BLAST, the JBrowse genome browser, ID conversion, heatmaps, and gene network analysis tools. Conclusions JCDB is the most comprehensive and well annotated knowledge base for J. curcas. We believe it will make a valuable contribution to the functional genomics study of J. curcas. The database is accessible at http://jcdb.xtbg.ac.cn.
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Affiliation(s)
- Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bang-Zhen Pan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Maosheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Wen Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.
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22
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Zhou T, Fan J, Zhao M, Zhang D, Li Q, Wang G, Zhang W, Cao F. Phenotypic variation of floral organs in Malus using frequency distribution functions. BMC PLANT BIOLOGY 2019; 19:574. [PMID: 31864283 PMCID: PMC6925448 DOI: 10.1186/s12870-019-2155-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Phenotypic diversity of floral organs plays an important role in plant systematic taxonomy and genetic variation studies. Previous research have focused on the direction of variation but disregarded its degree. Phenotypic variation (including directions and degrees) of 17 floral traits from wild to cultivated crabapples were explored by comparing their distributions and deviations in three different dimensions: floral organ number, size, and the shape. RESULTS Except for petal number, petal length / petal width, and sepal length / sepal width, the analyzed floral traits of cultivated crabapples all showed downward distributed box bodies in box plot analysis and left deviations of fitted curves in frequency distribution function analysis when compared to the wild, which revealed consistent variation directions of petaloid conversion (pistils or stamens → petals), size miniaturization (large → small), and shape narrowness (petal shape: circular → elliptic; sepal shape: triangular → lanceolate). However, only seven floral traits exhibited significant differences in box plot analysis, while all of the traits in frequency distribution function analysis were obviously offset. The variation degrees were quantitatively characterized by sizing traits > shaping traits > numbering traits and by horizontal dimensions > radial dimensions. CONCLUSIONS Frequency distribution function analysis was more sensitive than the box plot analysis, which constructed a theoretical basis for Malus flower type breeding and would provide a new quantitative method for future evaluation of floral variation among different groups of angiosperms at large.
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Affiliation(s)
- Ting Zhou
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Junjun Fan
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Department of Horticulture, University of Georgia, Athens, GA 30602 USA
| | - Mingming Zhao
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Yangzhou Crabapple Horticulture Company Limited, Yangzhou, 225200 China
| | - Donglin Zhang
- Department of Horticulture, University of Georgia, Athens, GA 30602 USA
| | - Qianhui Li
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Guibin Wang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Wangxiang Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Yangzhou Crabapple Horticulture Company Limited, Yangzhou, 225200 China
| | - Fuliang Cao
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
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Girma G, Natsume S, Carluccio AV, Takagi H, Matsumura H, Uemura A, Muranaka S, Takagi H, Stavolone L, Gedil M, Spillane C, Terauchi R, Tamiru M. Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling. PLoS One 2019; 14:e0216912. [PMID: 31545796 PMCID: PMC6756524 DOI: 10.1371/journal.pone.0216912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/05/2019] [Indexed: 01/03/2023] Open
Abstract
Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding.
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Affiliation(s)
- Gezahegn Girma
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Satoshi Natsume
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Anna Vittoria Carluccio
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Hiroki Takagi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Hideo Matsumura
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Aiko Uemura
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Satoru Muranaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Japan
- * E-mail:
| | - Hiroko Takagi
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Japan
| | - Livia Stavolone
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Melaku Gedil
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Ryohei Terauchi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Muluneh Tamiru
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
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Genome-wide analysis of spatiotemporal gene expression patterns during floral organ development in Brassica rapa. Mol Genet Genomics 2019; 294:1403-1420. [PMID: 31222475 DOI: 10.1007/s00438-019-01585-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/10/2019] [Indexed: 12/12/2022]
Abstract
Flowering is a key agronomic trait that directly influences crop yield and quality and serves as a model system for elucidating the molecular basis that controls successful reproduction, adaptation, and diversification of flowering plants. Adequate knowledge of continuous series of expression data from the floral transition to maturation is lacking in Brassica rapa. To unravel the genome expression associated with the development of early small floral buds (< 2 mm; FB2), early large floral buds (2-4 mm; FB4), stamens (STs) and carpels (CPs), transcriptome profiling was carried out with a Br300K oligo microarray. The results showed that at least 6848 known nonredundant genes (30% of the genes of the Br300K) were differentially expressed during the floral transition from vegetative tissues to maturation. Functional annotation of the differentially expressed genes (DEGs) (fold change ≥ 5) by comparison with a close relative, Arabidopsis thaliana, revealed 6552 unigenes (4579 upregulated; 1973 downregulated), including 131 Brassica-specific and 116 functionally known floral Arabidopsis homologs. Additionally, 1723, 236 and 232 DEGs were preferentially expressed in the tissues of STs, FB2, and CPs. These DEGs also included 43 transcription factors, mainly AP2/ERF-ERF, NAC, MADS-MIKC, C2H2, bHLH, and WRKY members. The differential gene expression during flower development induced dramatic changes in activities related to metabolic processes (23.7%), cellular (22.7%) processes, responses to the stimuli (7.5%) and reproduction (1%). A relatively large number of DEGs were observed in STs and were overrepresented by photosynthesis-related activities. Subsequent analysis via semiquantitative RT-PCR, histological analysis performed with in situ hybridization of BrLTP1 and transgenic reporter lines (BrLTP promoter::GUS) of B. rapa ssp. pekinensis supported the spatiotemporal expression patterns. Together, these results suggest that a temporally and spatially regulated process of the selective expression of distinct fractions of the same genome leads to the development of floral organs. Interestingly, most of the differentially expressed floral transcripts were located on chromosomes 3 and 9. This study generated a genome expression atlas of the early floral transition to maturation that represented the flowering regulatory elements of Brassica rapa.
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25
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Meng D, Cao Y, Chen T, Abdullah M, Jin Q, Fan H, Lin Y, Cai Y. Evolution and functional divergence of MADS-box genes in Pyrus. Sci Rep 2019; 9:1266. [PMID: 30718750 PMCID: PMC6362034 DOI: 10.1038/s41598-018-37897-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/12/2018] [Indexed: 02/02/2023] Open
Abstract
MADS-box transcription factors widely regulate all aspects of plant growth including development and reproduction. Although the MADS-box gene family genes have been extensively characterized in many plants, they have not been studied in closely related species. In this study, 73 and 74 MADS-box genes were identified in European pear (Pyrus communis) and Chinese pear (Pyrus bretschneideri), respectively. Based on the phylogenetic relationship, these genes could be clustered into five groups (Mα, Mβ, Mr, MIKCC, MIKC*) and the MIKCC group was further categorized into 10 subfamilies. The distribution of MADS-box genes on each chromosome was significantly nonrandom. Thirty-seven orthologs, twenty-five PcpMADS (P. communis MADS-box) paralogs and nineteen PbrMADS (P. bretschneideri MADS-box) paralogs were predicted. Among these paralogous genes, two pairs arose from tandem duplications (TD), nineteen from segmental duplication (SD) events and twenty-three from whole genome duplication (WGD) events, indicating SD/WGD events led to the expansion of MADS-box gene family. The MADS-box genes expression profiles in pear fruits indicated functional divergence and neo-functionalization or sub-functionalization of some orthologous genes originated from a common ancestor. This study provided a useful reference for further analysis the mechanisms of species differentiation and biodiversity formation among closely related species.
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Affiliation(s)
- Dandan Meng
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yunpeng Cao
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Tianzhe Chen
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Qing Jin
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Honghong Fan
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yi Lin
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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26
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Maheepala DC, Emerling CA, Rajewski A, Macon J, Strahl M, Pabón-Mora N, Litt A. Evolution and Diversification of FRUITFULL Genes in Solanaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:43. [PMID: 30846991 PMCID: PMC6394111 DOI: 10.3389/fpls.2019.00043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 01/11/2019] [Indexed: 05/12/2023]
Abstract
Ecologically and economically important fleshy edible fruits have evolved from dry fruit numerous times during angiosperm diversification. However, the molecular mechanisms that underlie these shifts are unknown. In the Solanaceae there has been a major shift to fleshy fruits in the subfamily Solanoideae. Evidence suggests that an ortholog of FRUITFULL (FUL), a transcription factor that regulates cell proliferation and limits the dehiscence zone in the silique of Arabidopsis, plays a similar role in dry-fruited Solanaceae. However, studies have shown that FUL orthologs have taken on new functions in fleshy fruit development, including regulating elements of tomato ripening such as pigment accumulation. FUL belongs to the core eudicot euFUL clade of the angiosperm AP1/FUL gene lineage. The euFUL genes fall into two paralogous clades, euFULI and euFULII. While most core eudicots have one gene in each clade, Solanaceae have two: FUL1 and FUL2 in the former, and MBP10 and MBP20 in the latter. We characterized the evolution of the euFUL genes to identify changes that might be correlated with the origin of fleshy fruit in Solanaceae. Our analyses revealed that the Solanaceae FUL1 and FUL2 clades probably originated through an early whole genome multiplication event. By contrast, the data suggest that the MBP10 and MBP20 clades are the result of a later tandem duplication event. MBP10 is expressed at weak to moderate levels, and its atypical short first intron lacks putative transcription factor binding sites, indicating possible pseudogenization. Consistent with this, our analyses show that MBP10 is evolving at a faster rate compared to MBP20. Our analyses found that Solanaceae euFUL gene duplications, evolutionary rates, and changes in protein residues and expression patterns are not correlated with the shift in fruit type. This suggests deeper analyses are needed to identify the mechanism underlying the change in FUL ortholog function.
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Affiliation(s)
- Dinusha C. Maheepala
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Christopher A. Emerling
- Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, École Pratique des Hautes Études, Montpellier, France
| | - Alex Rajewski
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Jenna Macon
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Maya Strahl
- The New York Botanical Garden, Bronx, NY, United States
| | | | - Amy Litt
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Amy Litt,
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27
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Pandey S, Goel R, Bhardwaj A, Asif MH, Sawant SV, Misra P. Transcriptome analysis provides insight into prickle development and its link to defense and secondary metabolism in Solanum viarum Dunal. Sci Rep 2018; 8:17092. [PMID: 30459319 PMCID: PMC6244164 DOI: 10.1038/s41598-018-35304-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022] Open
Abstract
Prickles are epidermal outgrowth found on the aerial surface of several terrestrial plants. Microscopic studies on prickles of S. viarum Dunal indicated a crucial role of glandular trichomes (GTs) in their development. A spontaneously obtained prickleless mutant showed normal epidermal GTs, but its downstream developmental process to prickle was perturbed. Thus, prickleless mutant offers an ideal opportunity to unveil molecular regulators working downstream to GTs in the prickle formation. Differential transcriptome analysis of epidermis of prickly and prickleless mutant revealed that expression of several defense regulators like ethylene, salicylic acid, PR-proteins, etc. were significantly down-regulated in prickleless mutant, provide an important link between defense and prickle development. It was also noteworthy that the expression of few essential development related TFs like MADS-box, R2R3-MYB, REM, DRL1, were also down-regulated in the stem, petioles, and leaves of prickleless mutant indicating their potential role in prickle development. Interestingly, the gene expression of terpenoid, steroid, flavonoid, glucosinolate, and lignin biosynthesis pathways were up-regulated in prickleless mutant. The biochemical and qRT-PCR analysis also confirmed metabolite elevation. These results indicated that the loss of prickle was compensated by elevated secondary metabolism in the prickleless mutant which played important role in the biotic and abiotic stress management.
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Affiliation(s)
- Shatrujeet Pandey
- Council of Scientific and Industrial Research - National Botanical Research Institute, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ridhi Goel
- Council of Scientific and Industrial Research - National Botanical Research Institute, Lucknow, 226001, India
| | - Archana Bhardwaj
- Council of Scientific and Industrial Research - National Botanical Research Institute, Lucknow, 226001, India
| | - Mehar H Asif
- Council of Scientific and Industrial Research - National Botanical Research Institute, Lucknow, 226001, India
| | - Samir V Sawant
- Council of Scientific and Industrial Research - National Botanical Research Institute, Lucknow, 226001, India.
| | - Pratibha Misra
- Council of Scientific and Industrial Research - National Botanical Research Institute, Lucknow, 226001, India.
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28
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Song GQ, Chen Q. Overexpression of the MADS-box gene K-domain increases the yield potential of blueberry. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:22-31. [PMID: 30348321 DOI: 10.1016/j.plantsci.2018.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/18/2018] [Accepted: 07/29/2018] [Indexed: 05/27/2023]
Abstract
MADS-box genes play a significant role for plant flowering. Keratin-like (K) domains are involved in protein-to-protein interactions in the formation of the MIKC-type MADS-box domain proteins. In this study, the potential of utilizing the K domain of a Vaccinium corymbosum SOC1-like gene (VcSOC1K) was investigated to modulate expression of other blueberry MADS-box genes for increasing blueberry productivity. Chilled transgenic blueberry plants overexpressing the VcSOC1K showed a significant increase in the number of canes, floral buds, and flower and fruit clusters compared to chilled non-transgenic plants. Additionally, nonchilled transgenic plants flowered whereas nonchilled non-transgenic plants did not. Transgenic plants showed an increase in tolerance to high soil pH. Comparative transcriptome analysis of transgenic and non-transgenic leaves showed differential expression of 17% of the MADS-box genes identified in blueberry. These differentially expressed (DE) MADS-box genes were associated with genes related to plant flowering, phytohormones, and response to various biotic and abiotic stimuli. The phenotypic changes and the DE MADS-box genes caused by the overexpression of VcSOC1K not only reveal that the MADS-box genes are involved in chilling/vernalization-mediated flowering in blueberry but also demonstrated that the overexpression of the K domain can effectively modulate plant reproductive processes.
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Affiliation(s)
- Guo-Qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
| | - Qiuxia Chen
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
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29
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Ma J, Shen X, Liu Z, Zhang D, Liu W, Liang H, Wang Y, He Z, Chen F. Isolation and Characterization of AGAMOUS-Like Genes Associated With Double-Flower Morphogenesis in Kerria japonica (Rosaceae). FRONTIERS IN PLANT SCIENCE 2018; 9:959. [PMID: 30050547 PMCID: PMC6052346 DOI: 10.3389/fpls.2018.00959] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 06/14/2018] [Indexed: 05/30/2023]
Abstract
Double-flower phenotype is more popular and attractive in garden and ornamental plants. There is great interest in exploring the molecular mechanisms underlying the double-flower formation for further breeding and selection. Kerria japonica, a commercial ornamental shrub of the Rosaceae family, is considered an excellent system to determine the mechanisms of morphological alterations, because it naturally has a single-flower form and double-flower variant with homeotic conversion of stamens into petals and carpels into leaf-like carpels. In this study, Sf-KjAG (AGAMOUS homolog of single-flower K. japonica) and Df-KjAG (AGAMOUS homolog of double-flower K. japonica) were isolated and characterized as two AGAMOUS (AG) homologs that occur strictly in single- and double-flower K. japonica, respectively. Our sequence comparison showed that Df-KjAG is derived from ectopic splicing with the insertion of a 2411 bp transposon-like fragment, which might disrupt mRNA accumulation and protein function, into intron 1. Ectopic expression analysis in Arabidopsis revealed that Sf-KjAG is highly conserved in specifying carpel and stamen identities. However, Df-KjAG did not show any putative C-class function in floral development. Moreover, yeast-two-hybrid assays showed that Sf-KjAG can interact with KjAGL2, KjAGL9, and KjAP1, whereas Df-KjAG has lost interactions with these floral identity genes. In addition, loss-of-function of Df-KjAG affected not only its own expression, but also that of other putative floral organ identity genes such as KjAGL2, KjAGL9, KjAP1, KjAP2, KjAP3, and KjPI. In conclusion, our findings suggest that double-flower formation in K. japonica can be attributed to Df-KjAG, which appears to be a mutant produced by the insertion of a transposon-like fragment in the normal AG homolog (Sf-KjAG) of single-flower K. japonica. Highlights:Sf-KjAG and Df-KjAG are different variations only distinguished by a transposon-like fragment insertion which lead to the evolutionary transformation from single-flower to double-flowers morphogenesis in Kerria japonica.
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Affiliation(s)
- Jiang Ma
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
- Forestry College, Beijing Forestry University, Beijing, China
| | - Xiangling Shen
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Zhixiong Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Wen Liu
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Hongwei Liang
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Yubing Wang
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Zhengquan He
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Faju Chen
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
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30
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Schorderet M, Duvvuru Muni RR, Fiebig A, Reinhardt D. Deregulation of MADS-box transcription factor genes in a mutant defective in the WUSCHEL-LIKE HOMEOBOX gene EVERGREEN of Petunia hybrida. PLANT SIGNALING & BEHAVIOR 2018; 13:e1471299. [PMID: 29995575 PMCID: PMC6207418 DOI: 10.1080/15592324.2018.1471299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 05/14/2023]
Abstract
Angiosperm inflorescences develop in two fundamentally different ways. In monopodial plants, for example in Arabidopsis thaliana, the flowers are initiated as lateral appendages of a central indeterminate inflorescence meristem. In sympodial plants, flowers arise by terminal differentiation of the inflorescence meristem, while further inflorescence development proceeds from new sympodial meristems that are generated at the flank of the terminal flower. We have used the sympodial model species Petunia hybrida to investigate inflorescence development. Here, we describe a mutant, bonsai (bns), which is defective in flower formation, inflorescence branching, and control of meristem size. Detailed microscopic analysis revealed that bns meristems retain vegetative charateristics including spiral phyllotaxis. Consistent with a block in flower formation, bns mutants exhibit a deregulated expression of various MADS-box genes. Molecular analysis revealed that the bns mutant carries a transposon insertion in the previously described EVERGREEN (EVG) gene, which belongs to the WUSCHEL-LIKE HOMEOBOX (WOX) transcription factor gene family. EVG falls in the WOX9 subfamily, which has diverse developmental functions in angiosperms. The comparison of WOX9 orthologues in five model species for flowering shows that these genes play functionally divergent roles in monopodial and sympodial plants, indicating that the WOX9 regulatory node may have played an important role in the evolution of shoot architecture.
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Affiliation(s)
- M. Schorderet
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
| | - R. R. Duvvuru Muni
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
- Monsanto Holdings Private Limited, Mfar Manyata Tech Park, Nagavara, Bangalore, India
| | - A. Fiebig
- Research Group Bioinformatics and Information Technology, Department Breeding Research, Leibniz Institute of Plant Genetics and CropPlant Research (IPK) Gatersleben, Seeland, Germany
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Coenen H, Viaene T, Vandenbussche M, Geuten K. TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms. BMC PLANT BIOLOGY 2018; 18:129. [PMID: 29929474 PMCID: PMC6013966 DOI: 10.1186/s12870-018-1349-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND MADS-box genes are key regulators of plant reproductive development and members of most lineages of this gene family have been extensively studied. However, the function and diversification of the ancient TM8 lineage remains elusive to date. The available data suggest a possible function in flower development in tomato and fast evolution through numerous gene loss events in flowering plants. RESULTS We show the broad conservation of TM8 within angiosperms and find that in contrast to other MADS-box gene lineages, no gene duplicates have been retained after major whole genome duplication events. Through knock-down of NbTM8 by virus induced gene silencing in Nicotiana benthamiana, we show that NbTM8 represses miR172 together with another MADS-box gene, SHORT VEGETATIVE PHASE (NbSVP). In the closely related species Petunia hybrida, PhTM8 is not expressed under the conditions we investigated and consistent with this, a knock-out mutant did not show a phenotype. Finally, we generated transgenic tomato plants in which TM8 was silenced or ectopically expressed, but these plants did not display a clear phenotype. Therefore, no clear function could be confirmed for Solanum lycopersium. CONCLUSIONS While the presence of TM8 is generally conserved, it remains difficult to propose a general function in angiosperms. Based on all the available data to date, supplemented with our own results, TM8 function seems to have diversified quickly throughout angiosperms and acts as repressor of miR172 in Nicotiana benthamiana, together with NbSVP.
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Affiliation(s)
- Heleen Coenen
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Tom Viaene
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes, University Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Koen Geuten
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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Mohanty JN, Joshi RK. Molecular cloning, characterization and expression analysis of MADS-box genes associated with reproductive development in Momordica dioica Roxb. 3 Biotech 2018; 8:150. [PMID: 29616182 DOI: 10.1007/s13205-018-1176-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/19/2018] [Indexed: 02/03/2023] Open
Abstract
The repertoire and functions of MADS-box family transcription factors (TFs) largely remains unexplored with respect to floral organogenesis of Momordica dioica Roxb. Degenerative PCR followed by rapid amplification of cDNA ends was employed in the present study to clone and characterize 17 MADS-box genes (designated as MdMADS01 to MdMADS17) from the floral buds of M. dioica. The cloned genes were clustered into three subgroups (11 MIKCC, 4 MIKC* and 2 Mα) based on phylogenetic relationships with the MADS-box genes from Cucumis sativus, Cucumis melo and Arabidopsis thaliana. Southern hybridization showed that all the isolated genes were represented by single copy locus in the M. dioica genome. Gene structure analysis revealed 1-8 exons in MdMADS-box genes with the number of exons in MIKC greatly exceeding from that in M-type genes. Motif elicitation of the MdMADS-box genes indicated the presence of additional domains with MIKC type, suggesting that they had more complex structures. Expression analysis of MdMADS genes in six M. dioica transcriptome suggested that, 11 MIKCC-type genes are associated with floral homeotic functions, 4 MIKC*-type genes (MdMADS12 to MdMADS15) controlled the growth of male gametophyte, while the two M-type genes (MdMADS16 and MdMADS17) played significant role in female gametogenesis and seed development. Overall, these are the first set of MADS-box genes from M. dioica exhibiting a differential expression pattern during floral development. The results from this study will provide valuable information for further functional studies of candidate MADS-box genes in the sexual dimorphism of this economically important dioecious cucurbit.
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Hui WK, Wang Y, Chen XY, Zayed MZ, Wu GJ. Analysis of Transcriptional Responses of the Inflorescence Meristems in Jatropha curcas Following Gibberellin Treatment. Int J Mol Sci 2018; 19:ijms19020432. [PMID: 29389867 PMCID: PMC5855654 DOI: 10.3390/ijms19020432] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/16/2018] [Accepted: 01/25/2018] [Indexed: 12/25/2022] Open
Abstract
Jatropha curcas L. seeds an oilseed plant with great potential for biodiesel production. However, low seed yield, which was limited by its lower female flowers, was a major drawback for its utilization. Our previous study found that the flower number and female-to-male ratio were increased by gibberellin treatment. Here, we compared the transcriptomic profiles of inflorescence meristem at different time points after gibberellic acid A3 (GA3) treatment. The present study showed that 951 differentially expressed genes were obtained in response to gibberellin treatment, compared with control samples. The 6-h time point was an important phase in the response to exogenous gibberellin. Furthermore, the plant endogenous gibberellin, auxin, ethylene, abscisic acid, and brassinolide-signaling transduction pathways were repressed, whereas the genes associated with cytokinin and jasmonic acid signaling were upregulated for 24-h time point following GA3 treatment. In addition, the floral meristem determinacy genes (JcLFY, JcSOC1) and floral organ identity genes (JcAP3, JcPI, JcSEP1-3) were significantly upregulated, but their negative regulator (JcSVP) was downregulated after GA3 treatment. Moreover, the effects of phytohormone, which was induced by exogenous plant growth regulator, mainly acted on the female floral differentiation process. To the best of our knowledge, this data is the first comprehensive analysis of the underlying transcriptional response mechanism of floral differentiation following GA3 treatment in J. curcas, which helps in engineering high-yielding varieties of Jatropha.
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Affiliation(s)
- Wen-Kai Hui
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
| | - Xiao-Yang Chen
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
| | - Mohamed Zaky Zayed
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
- Forestry and Wood Technology Department, Faculty of Agriculture (EL-Shatby), Alexandria University, Alexandria 21527, Egypt.
| | - Guo-Jiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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Monniaux M, Vandenbussche M. How to Evolve a Perianth: A Review of Cadastral Mechanisms for Perianth Identity. FRONTIERS IN PLANT SCIENCE 2018; 9:1573. [PMID: 30420867 PMCID: PMC6216099 DOI: 10.3389/fpls.2018.01573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/09/2018] [Indexed: 05/12/2023]
Abstract
The flower of angiosperms is considered to be a major evolutionary innovation that impacted the whole biome. In particular, two properties of the flower are classically linked to its ecological success: bisexuality and a differentiated perianth with sepals and petals. Although the molecular basis for floral organ identity is well understood in extant species and summarized in the famous ABC model, how perianth identity appeared during evolution is still unknown. Here we propose that cadastral mechanisms that maintain reproductive organ identities to the center of the flower could have supported perianth evolution. In particular, repressing B- and C-class genes expression toward the inner whorls of the flower, is a key process to isolate domains with sepal and petal identity in the outer whorls. We review from the literature in model species the diverse regulators that repress B- and C-class genes expression to the center of the flower. This review highlights the existence of both unique and conserved repressors between species, and possible candidates to investigate further in order to shed light on perianth evolution.
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Hui W, Yang Y, Wu G, Peng C, Chen X, Zayed MZ. Transcriptome profile analysis reveals the regulation mechanism of floral sex differentiation in Jatropha curcas L. Sci Rep 2017; 7:16421. [PMID: 29180629 PMCID: PMC5703882 DOI: 10.1038/s41598-017-16545-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/14/2017] [Indexed: 01/21/2023] Open
Abstract
The seeds of Jatropha curcas contain a high percentage of biodiesel. However, low seed yield which was limited by its poor female flowers was a bottleneck for its utilization. Here, we compared the transcriptomic profiles of five different samples during floral sex differentiation stages using Illumina Hiseq 4000. Our results showed that hundreds of differentially expressed genes (DEGs) were detected in floral sex initiation period, but thousands of DEGs were involved in the stamens and ovules development process. Moreover, the DEGs were mainly shown up-regulation in male floral initiation, but mainly down-regulation in female floral initiation. Male floral initiation was associated with the flavonoid biosynthesis pathway while female floral initiation was related to the phytohormone signal transduction pathway. Cytokinin (CTK) signaling triggered the initiation of female floral primordium, thereafter other phytohormones co-promoted the female floral development. In addition, the floral organ identity genes played important roles in floral sex differentiation process and displayed a general conservation of the ABCDE model in J. curcas. To the best of our knowledge, this data is the first comprehensive analysis of the underlying regulatory mechanism and the related genes during floral sex differentiation in J. curcas, which help in engineering high-yielding varieties of J. curcas.
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Affiliation(s)
- Wenkai Hui
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, P.R. China
| | - Yuantong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Changcao Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Xiaoyang Chen
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, P.R. China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China.
| | - Mohamed Zaky Zayed
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China.,Forestry and Wood Technology Department, Faculty of Agriculture (EL-Shatby), Alexandria University, Alexandria, Egypt
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Mao Y, Liu W, Chen X, Xu Y, Lu W, Hou J, Ni J, Wang Y, Wu L. Flower Development and Sex Determination between Male and Female Flowers in Vernicia fordii. FRONTIERS IN PLANT SCIENCE 2017; 8:1291. [PMID: 28775735 PMCID: PMC5517574 DOI: 10.3389/fpls.2017.01291] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/07/2017] [Indexed: 05/30/2023]
Abstract
Vernicia fordii is a monoecious and diclinous species with male and female flowers on the same inflorescence. Low female to male flower ratio is one of the main reasons for low yield in this species. However, little is known of its floral development and sex determination. Here, according to the results of scanning electron microscopy and histological analysis, the floral development of V. fordii was divided into 12 stages and the first morphological divergence between the male and female flowers was found to occur at stage 7. The male flowers are always unisexual, but the female flowers present bisexual characteristics, with sterile stamen (staminode) restricted to pre-meiosis of mother sporogenous cells and cell death occurring at later development stages. To further elucidate the molecular mechanism underling sex determination at the divergence stage for male and female flowers, comparative transcriptome analysis was performed. In total, 56,065 unigenes were generated and 608 genes were differentially expressed between male and female flowers, among which 310 and 298 DEGs (differentially expressed genes) showed high expression levels in males and females, respectively. The transcriptome data showed that the sexual dimorphism of female flowers was affected by jasmonic acid, transcription factors, and some genes related to the floral meristem activity. Ten candidate genes showed consistent expression in the qRT-PCR validation and DEGs data. In this study, we provide developmental characterization and transcriptomic information for better understanding of the development of unisexual flowers and the regulatory networks underlying the mechanism of sex determination in V. fordii, which would be helpful in the molecular breeding of V. fordii to improve the yield output.
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Affiliation(s)
- Yingji Mao
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
- School of Life Science, University of Science and Technology of ChinaHefei, China
| | - Wenbo Liu
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
- School of Life Science, University of Science and Technology of ChinaHefei, China
| | - Xue Chen
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
- School of Life Science, University of Science and Technology of ChinaHefei, China
| | - Yang Xu
- Biotechnology Center, Anhui Agriculture UniversityHefei, China
| | - Weili Lu
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
- School of Life Science, University of Science and Technology of ChinaHefei, China
- School of Pharmacy, Anhui Medical UniversityHefei, China
| | - Jinyan Hou
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
| | - Jun Ni
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
| | - Yuting Wang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
- School of Life Science, University of Science and Technology of ChinaHefei, China
- The Sericultural Research Institute, Anhui Academy of Agricultural ScienceHefei, China
| | - Lifang Wu
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of SciencesHefei, China
- School of Life Science, University of Science and Technology of ChinaHefei, China
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Kitazawa Y, Iwabuchi N, Himeno M, Sasano M, Koinuma H, Nijo T, Tomomitsu T, Yoshida T, Okano Y, Yoshikawa N, Maejima K, Oshima K, Namba S. Phytoplasma-conserved phyllogen proteins induce phyllody across the Plantae by degrading floral MADS domain proteins. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2799-2811. [PMID: 28505304 PMCID: PMC5853863 DOI: 10.1093/jxb/erx158] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/13/2017] [Indexed: 05/21/2023]
Abstract
ABCE-class MADS domain transcription factors (MTFs) are key regulators of floral organ development in angiosperms. Aberrant expression of these genes can result in abnormal floral traits such as phyllody. Phyllogen is a virulence factor conserved in phytoplasmas, plant pathogenic bacteria of the class Mollicutes. It triggers phyllody in Arabidopsis thaliana by inducing degradation of A- and E-class MTFs. However, it is still unknown whether phyllogen can induce phyllody in plants other than A. thaliana, although phytoplasma-associated phyllody symptoms are observed in a broad range of angiosperms. In this study, phyllogen was shown to cause phyllody phenotypes in several eudicot species belonging to three different families. Moreover, phyllogen can interact with MTFs of not only angiosperm species including eudicots and monocots but also gymnosperms and a fern, and induce their degradation. These results suggest that phyllogen induces phyllody in angiosperms and inhibits MTF function in diverse plant species.
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Affiliation(s)
- Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Misako Himeno
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Momoka Sasano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Takamichi Nijo
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tatsuya Tomomitsu
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tetsuya Yoshida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Yukari Okano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Nobuyuki Yoshikawa
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka-shi, Iwate, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Kenro Oshima
- Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei-shi, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
- Correspondence:
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Chen F, Zhang X, Liu X, Zhang L. Evolutionary Analysis of MIKC c-Type MADS-Box Genes in Gymnosperms and Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:895. [PMID: 28611810 PMCID: PMC5447709 DOI: 10.3389/fpls.2017.00895] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/12/2017] [Indexed: 05/02/2023]
Abstract
MIKCc-type MADS-box genes encode transcription factors that control floral organ morphogenesis and flowering time in flowering plants. Here, in order to determine when the subfamilies of MIKCc originated and their early evolutionary trajectory, we sampled and analyzed the genomes and large-scale transcriptomes representing all the orders of gymnosperms and basal angiosperms. Through phylogenetic inference, the MIKCc-type MADS-box genes were subdivided into 14 monophyletic clades. Among them, the gymnosperm orthologs of AGL6, SEP, AP1, GMADS, SOC1, AGL32, AP3/PI, SVP, AGL15, ANR1, and AG were identified. We identified and characterized the origin of a novel subfamily GMADS within gymnosperms but lost orthologs in monocots and Brassicaceae. ABCE model prototype genes were relatively conserved in terms of gene number in gymnosperms, but expanded in angiosperms, whereas SVP, SOC1, and GMADS had dramatic expansions in gymnosperms but conserved in angiosperms. Our results provided the most detailed evolutionary history of all MIKCc gene clades in gymnosperms and angiosperms. We proposed that although the near complete set of MIKCc genes had evolved in gymnosperms, the duplication and expressional transition of ABCE model MIKCc genes in the ancestor of angiosperms triggered the first flower.
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Yan H, Zhang H, Wang Q, Jian H, Qiu X, Baudino S, Just J, Raymond O, Gu L, Wang J, Bendahmane M, Tang K. The Rosa chinensis cv. Viridiflora Phyllody Phenotype Is Associated with Misexpression of Flower Organ Identity Genes. FRONTIERS IN PLANT SCIENCE 2016; 7:996. [PMID: 27462328 PMCID: PMC4941542 DOI: 10.3389/fpls.2016.00996] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 06/24/2016] [Indexed: 05/21/2023]
Abstract
Phyllody is a flower abnormality in which leaf-like structures replace flower organs in all whorls. Here, we investigated the origin and the molecular mechanism of phyllody phenotype in Rosa chinensis cv. Viridiflora, an ancient naturally occurring Chinese mutant cultivar. Reciprocal grafting experiments and microscopy analyses, demonstrated that the phyllody phenotype in Viridiflora is not associated with phytoplasmas infection. Transcriptome comparisons by the mean of RNA-Seq identified 672 up-regulated and 666 down-regulated genes in Viridiflora compared to its closely related genotype R. chinensis cv. Old Blush. A fraction of these genes are putative homologs of genes known to be involved in flower initiation and development. We show that in flower whorl 2 of Viridiflora, a down-regulation of the floral organ identity genes RcPISTILLATA (RcPI), RcAPETALA3 (RcAP3) and RcSEPALLATA3 (RcSEP3), together with an up-regulation of the putative homolog of the gene SUPPRESSOR of OVEREXPRESSION of CONSTANS1 (RcSOC1) are likely at the origin of the loss of petal identity and leaf-like structures formation. In whorl 3 of Viridiflora, ectopic expression of RcAPETALA2 (RcAP2) along with the down regulation of RcPI, RcAP3, and RcSEP3 is associated with loss of stamens identity and leaf-like structures formation. In whorl 4, the ectopic expression of RcAP2 associated with a down-regulation of RcSEP3 and of the C-class gene RcAGAMOUS correlate with loss of pistil identity. The latter also suggested the antagonist effect between the A and C class genes in the rose. Together, these data suggest that modified expression of the ABCE flower organ identity genes is associated with the phyllody phenotype in the rose Viridiflora and that these genes are important for normal flower organs development.
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Affiliation(s)
- Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Hao Zhang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Qigang Wang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Hongying Jian
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Xianqin Qiu
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Sylvie Baudino
- Université de Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727Saint-Etienne, France
| | - Jeremy Just
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRALyon, France
| | - Olivier Raymond
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRALyon, France
| | - Lianfeng Gu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Mohammed Bendahmane
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRALyon, France
| | - Kaixue Tang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
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Shorinola O, Bird N, Simmonds J, Berry S, Henriksson T, Jack P, Werner P, Gerjets T, Scholefield D, Balcárková B, Valárik M, Holdsworth MJ, Flintham J, Uauy C. The wheat Phs-A1 pre-harvest sprouting resistance locus delays the rate of seed dormancy loss and maps 0.3 cM distal to the PM19 genes in UK germplasm. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4169-78. [PMID: 27217549 PMCID: PMC5301926 DOI: 10.1093/jxb/erw194] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The precocious germination of cereal grains before harvest, also known as pre-harvest sprouting, is an important source of yield and quality loss in cereal production. Pre-harvest sprouting is a complex grain defect and is becoming an increasing challenge due to changing climate patterns. Resistance to sprouting is multi-genic, although a significant proportion of the sprouting variation in modern wheat cultivars is controlled by a few major quantitative trait loci, including Phs-A1 in chromosome arm 4AL. Despite its importance, little is known about the physiological basis and the gene(s) underlying this important locus. In this study, we characterized Phs-A1 and show that it confers resistance to sprouting damage by affecting the rate of dormancy loss during dry seed after-ripening. We show Phs-A1 to be effective even when seeds develop at low temperature (13 °C). Comparative analysis of syntenic Phs-A1 intervals in wheat and Brachypodium uncovered ten orthologous genes, including the Plasma Membrane 19 genes (PM19-A1 and PM19-A2) previously proposed as the main candidates for this locus. However, high-resolution fine-mapping in two bi-parental UK mapping populations delimited Phs-A1 to an interval 0.3 cM distal to the PM19 genes. This study suggests the possibility that more than one causal gene underlies this major pre-harvest sprouting locus. The information and resources reported in this study will help test this hypothesis across a wider set of germplasm and will be of importance for breeding more sprouting resilient wheat varieties.
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Affiliation(s)
| | - Nicholas Bird
- John Innes Centre, Norwich Research Park, NR4 7UH, UK KWS UK Ltd, Hertfordshire, SG8 7RE, UK
| | | | - Simon Berry
- Limagrain UK Ltd, Woolpit Business Park, IP30 9UP, UK
| | | | | | | | - Tanja Gerjets
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - Duncan Scholefield
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - Barbara Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - M J Holdsworth
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - John Flintham
- John Innes Centre, Norwich Research Park, NR4 7UH, UK
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Liu H, Sun M, Du D, Pan H, Cheng T, Wang J, Zhang Q, Gao Y. Whole-transcriptome analysis of differentially expressed genes in the ray florets and disc florets of Chrysanthemum morifolium. BMC Genomics 2016; 17:398. [PMID: 27225275 PMCID: PMC4881213 DOI: 10.1186/s12864-016-2733-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 05/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chrysanthemum morifolium is one of the most important global cut flower and pot plants, and has been cultivated worldwide. However, limited genomic resources are available and the molecular mechanisms involved in the two morphologically distinct floret developmental cycles in chrysanthemum remain unclear. RESULTS The transcriptomes of chrysanthemum ray florets, disc florets and leaves were sequenced using Illumina paired-end sequencing technology. In total, 16.9 G reads were assembled into 93,138 unigenes with an average length of 738 bp, of which 44,364 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 26,320, 22,304 and 13,949 unigenes were assigned to 54 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 280 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1863 differentially expressed genes (DEGs) (1210 up-regulated and 653 down-regulated) were identified between ray florets and disc florets, including genes encoding transcription factors and protein kinases. GO and KEGG pathway enrichment analyses were performed on the DEGs to identify differences in the biological processes and pathways between ray florets and disc florets. The important regulatory genes controlling flower development and flower organ determination, as well as important functional genes in the anthocyanin biosynthetic pathway, were identified, of which two leucoanthocyanidin dioxygenase-encoding genes showed specific expression in ray florets. Lastly, reverse transcription quantitative PCR was conducted to validate the DEGs identified in our study. CONCLUSIONS Comparative transcriptome analysis revealed significant differences in patterns of gene expression and signaling pathways between ray florets and disc florets in Chrysanthemum morifolium. This study provided the first step to understanding the molecular mechanism of the differential development of ray florets and disc florets in chrysanthemum, and also provided valuable genomic resources for candidate genes applicable for the breeding of novel varieties in chrysanthemum.
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Affiliation(s)
- Hua Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ming Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Dongliang Du
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| | - Yike Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
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Baba SA, Mohiuddin T, Basu S, Swarnkar MK, Malik AH, Wani ZA, Abbas N, Singh AK, Ashraf N. Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis. BMC Genomics 2015; 16:698. [PMID: 26370545 PMCID: PMC4570256 DOI: 10.1186/s12864-015-1894-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/01/2015] [Indexed: 11/30/2022] Open
Abstract
Background Crocus sativus stigmas form rich source of apocarotenoids like crocin, picrocrocin and saffranal which besides imparting color, flavour and aroma to saffron spice also have tremendous pharmacological properties. Inspite of their importance, the biosynthetic pathway of Crocus apocarotenoids is not fully elucidated. Moreover, the mechanism of their stigma specific accumulation remains unknown. Therefore, deep transcriptome sequencing of Crocus stigma and rest of the flower tissue was done to identify the genes and transcriptional regulators involved in the biosynthesis of these compounds. Results Transcriptome of stigma and rest of the flower tissue was sequenced using Illumina Genome Analyzer IIx platform which generated 64,604,402 flower and 51,350,714 stigma reads. Sequences were assembled de novo using trinity resulting in 64,438 transcripts which were classified into 32,204 unigenes comprising of 9853 clusters and 22,351 singletons. A comprehensive functional annotation and gene ontology (GO) analysis was carried out. 58.5 % of the transcripts showed similarity to sequences present in public databases while rest could be specific to Crocus. 5789 transcripts showed similarity to transcription factors representing 76 families out of which Myb family was most abundant. Many genes involved in carotenoid/apocarotenoid pathway were identified for the first time in this study which includes zeta-carotene isomerase and desaturase, carotenoid isomerase and lycopene epsilon-cyclase. GO analysis showed that the predominant classes in biological process category include metabolic process followed by cellular process and primary metabolic process. KEGG mapping analysis indicated that pathways involved in ribosome, carbon and starch and sucrose metabolism were highly represented. Differential expression analysis indicated that key carotenoid/apocarotenoid pathway genes including phytoene synthase, phytoene desaturase and carotenoid cleavage dioxygenase 2 are enriched in stigma thereby providing molecular proof for stigma to be the site of apocarotenoid biosynthesis. Conclusions This data would provide a rich source for understanding the carotenoid/apocarotenoid metabolism in Crocus. The database would also help in investigating many questions related to saffron biology including flower development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1894-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shoib Ahmad Baba
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Tabasum Mohiuddin
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Swaraj Basu
- Stazione Zoologica Anton Dohrn di Napoli, Naples, Italy.
| | - Mohit Kumar Swarnkar
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
| | - Aubid Hussain Malik
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Zahoor Ahmed Wani
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
| | - Nazia Abbas
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India.
| | - Anil Kumar Singh
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
| | - Nasheeman Ashraf
- Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India.
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Phylogenomics reveals surprising sets of essential and dispensable clades of MIKCc-group MADS-box genes in flowering plants. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:353-62. [DOI: 10.1002/jez.b.22598] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 09/02/2014] [Indexed: 11/07/2022]
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Wells CE, Vendramin E, Jimenez Tarodo S, Verde I, Bielenberg DG. A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]. BMC PLANT BIOLOGY 2015; 15:41. [PMID: 25848674 PMCID: PMC4329201 DOI: 10.1186/s12870-015-0436-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 01/22/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes. RESULTS We identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248 ± 72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 and FLC lineages in woody perennial species. CONCLUSIONS Most Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.
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Affiliation(s)
- Christina E Wells
- />Department of Biological Sciences, Clemson University, Long Hall, 29634 Clemson, SC USA
| | - Elisa Vendramin
- />Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria, Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | - Sergio Jimenez Tarodo
- />School of Agriculture, Forestry and Life Sciences, Clemson University, Poole Agricultural Center, 29634 Clemson, SC USA
| | - Ignazio Verde
- />Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria, Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | - Douglas G Bielenberg
- />Department of Biological Sciences, Clemson University, Long Hall, 29634 Clemson, SC USA
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Daminato M, Masiero S, Resentini F, Lovisetto A, Casadoro G. Characterization of TM8, a MADS-box gene expressed in tomato flowers. BMC PLANT BIOLOGY 2014; 14:319. [PMID: 25433802 PMCID: PMC4258831 DOI: 10.1186/s12870-014-0319-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/06/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND The identity of flower organs is specified by various MIKC MADS-box transcription factors which act in a combinatorial manner. TM8 is a MADS-box gene that was isolated from the floral meristem of a tomato mutant more than twenty years ago, but is still poorly known from a functional point of view in spite of being present in both Angiosperms and Gymnosperms, with some species harbouring more than one copy of the gene. This study reports a characterization of TM8 that was carried out in transgenic tomato plants with altered expression of the gene. RESULTS Tomato plants over-expressing either TM8 or a chimeric repressor form of the gene (TM8:SRDX) were prepared. In the TM8 up-regulated plants it was possible to observe anomalous stamens with poorly viable pollen and altered expression of several floral identity genes, among them B-, C- and E-function ones, while no apparent morphological modifications were visible in the other whorls. Oblong ovaries and fruits, that were also parthenocarpic, were obtained in the plants expressing the TM8:SRDX repressor gene. Such ovaries showed modified expression of various carpel-related genes. No apparent modifications could be seen in the other flower whorls. The latter plants had also epinastic leaves and malformed flower abscission zones. By using yeast two hybrid assays it was possible to show that TM8 was able to interact in yeast with MACROCALIX. CONCLUSIONS The impact of the ectopically altered TM8 expression on the reproductive structures suggests that this gene plays some role in the development of the tomato flower. MACROCALYX, a putative A-function MADS-box gene, was expressed in all the four whorls of fully developed flowers, and showed quantitative variations that were opposite to those of TM8 in the anomalous stamens and ovaries. Since the TM8 protein interacted in vitro only with the A-function MADS-box protein MACROCALYX, it seems that for the correct differentiation of the tomato reproductive structures possible interactions between TM8 and MACROCALYX proteins might be important.
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Affiliation(s)
- Margherita Daminato
- />Department of Biology, University of Padua, Via G. Colombo, 3, 35131 Padua, Italy
| | - Simona Masiero
- />Department of Bioscience, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Francesca Resentini
- />Department of Bioscience, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Alessandro Lovisetto
- />Department of Biology, University of Padua, Via G. Colombo, 3, 35131 Padua, Italy
| | - Giorgio Casadoro
- />Department of Biology, University of Padua, Via G. Colombo, 3, 35131 Padua, Italy
- />Botanical Garden, University of Padua, Via Orto Botanico, 15, 35123 Padua, Italy
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Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. ANNALS OF BOTANY 2014; 114:1545-53. [PMID: 24973416 PMCID: PMC4204783 DOI: 10.1093/aob/mcu123] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/29/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND WOX (Wuschel-like homeobOX) genes form a family of plant-specific HOMEODOMAIN transcription factors, the members of which play important developmental roles in a diverse range of processes. WOX genes were first identified as determining cell fate during embryo development, as well as playing important roles in maintaining stem cell niches in the plant. In recent years, new roles have been identified in plant architecture and organ development, particularly at the flower level. SCOPE In this review, the role of WOX genes in flower development and flower architecture is highlighted, as evidenced from data obtained in the last few years. The roles played by WOX genes in different species and different flower organs are compared, and differential functional recruitment of WOX genes during flower evolution is considered. CONCLUSIONS This review compares available data concerning the role of WOX genes in flower and organ architecture among different species of angiosperms, including representatives of monocots and eudicots (rosids and asterids). These comparative data highlight the usefulness of the WOX gene family for evo-devo studies of floral development.
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Affiliation(s)
- Enrico Costanzo
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Christophe Trehin
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
| | - Michiel Vandenbussche
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
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Serwatowska J, Roque E, Gómez-Mena C, Constantin GD, Wen J, Mysore KS, Lund OS, Johansen E, Beltrán JP, Cañas LA. Two euAGAMOUS genes control C-function in Medicago truncatula. PLoS One 2014; 9:e103770. [PMID: 25105497 PMCID: PMC4126672 DOI: 10.1371/journal.pone.0103770] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/02/2014] [Indexed: 02/07/2023] Open
Abstract
C-function MADS-box transcription factors belong to the AGAMOUS (AG) lineage and specify both stamen and carpel identity and floral meristem determinacy. In core eudicots, the AG lineage is further divided into two branches, the euAG and PLE lineages. Functional analyses across flowering plants strongly support the idea that duplicated AG lineage genes have different degrees of subfunctionalization of the C-function. The legume Medicago truncatula contains three C-lineage genes in its genome: two euAG genes (MtAGa and MtAGb) and one PLENA-like gene (MtSHP). This species is therefore a good experimental system to study the effects of gene duplication within the AG subfamily. We have studied the respective functions of each euAG genes in M. truncatula employing expression analyses and reverse genetic approaches. Our results show that the M. truncatula euAG- and PLENA-like genes are an example of subfunctionalization as a result of a change in expression pattern. MtAGa and MtAGb are the only genes showing a full C-function activity, concomitant with their ancestral expression profile, early in the floral meristem, and in the third and fourth floral whorls during floral development. In contrast, MtSHP expression appears late during floral development suggesting it does not contribute significantly to the C-function. Furthermore, the redundant MtAGa and MtAGb paralogs have been retained which provides the overall dosage required to specify the C-function in M. truncatula.
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Affiliation(s)
- Joanna Serwatowska
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Gabriela D. Constantin
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America
| | - Kirankumar S. Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America
| | - Ole S. Lund
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - Elisabeth Johansen
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - José Pío Beltrán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Luis A. Cañas
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
- * E-mail:
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Xu Z, Zhang Q, Sun L, Du D, Cheng T, Pan H, Yang W, Wang J. Genome-wide identification, characterisation and expression analysis of the MADS-box gene family in Prunus mume. Mol Genet Genomics 2014; 289:903-20. [PMID: 24859011 DOI: 10.1007/s00438-014-0863-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 05/06/2014] [Indexed: 11/29/2022]
Abstract
MADS-box genes encode transcription factors that play crucial roles in plant development, especially in flower and fruit development. To gain insight into this gene family in Prunus mume, an important ornamental and fruit plant in East Asia, and to elucidate their roles in flower organ determination and fruit development, we performed a genome-wide identification, characterisation and expression analysis of MADS-box genes in this Rosaceae tree. In this study, 80 MADS-box genes were identified in P. mume and categorised into MIKC, Mα, Mβ, Mγ and Mδ groups based on gene structures and phylogenetic relationships. The MIKC group could be further classified into 12 subfamilies. The FLC subfamily was absent in P. mume and the six tandemly arranged DAM genes might experience a species-specific evolution process in P. mume. The MADS-box gene family might experience an evolution process from MIKC genes to Mδ genes to Mα, Mβ and Mγ genes. The expression analysis suggests that P. mume MADS-box genes have diverse functions in P. mume development and the functions of duplicated genes diverged after the duplication events. In addition to its involvement in the development of female gametophytes, type I genes also play roles in male gametophytes development. In conclusion, this study adds to our understanding of the roles that the MADS-box genes played in flower and fruit development and lays a foundation for selecting candidate genes for functional studies in P. mume and other species. Furthermore, this study also provides a basis to study the evolution of the MADS-box family.
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Affiliation(s)
- Zongda Xu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua east road, Haidian district, Beijing, 100083, China
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Dreni L, Kater MM. MADS reloaded: evolution of the AGAMOUS subfamily genes. THE NEW PHYTOLOGIST 2014; 201:717-732. [PMID: 24164649 DOI: 10.1111/nph.12555] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/02/2013] [Indexed: 05/03/2023]
Abstract
AGAMOUS subfamily proteins are encoded by MADS-box family genes. They have been shown to play key roles in the determination of reproductive floral organs such as stamens, carpels and ovules. However, they also play key roles in ensuring a fixed number of floral organs by controlling floral meristem determinacy. Recently, an enormous amount of sequence data for nonmodel species have become available together with functional data on AGAMOUS subfamily members in many species. Here, we give a detailed overview of the most important information about this interesting gene subfamily and provide new insights into its evolution.
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Affiliation(s)
- Ludovico Dreni
- Department of Biosciences, Università degli Studi di Milano, via Celoria 26, 20133, Milan, Italy
| | - Martin M Kater
- Department of Biosciences, Università degli Studi di Milano, via Celoria 26, 20133, Milan, Italy
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Merging Ecology and Genomics to Dissect Diversity in Wild Tomatoes and Their Relatives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:273-98. [DOI: 10.1007/978-94-007-7347-9_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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